{ "type": "genome", "identifier": "GCF_014287925.1", "organism": "Clostridium segne", "title": "Clostridium segne", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MRCEN World Data Centre for Microoganisms(WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014287925.1", "bioproject": "PRJNA224116", "biosample": "SAMN15807795", "wgs_master": "JACOOW000000000.1", "refseq_category": "reference genome", "taxid": "2763038", "species_taxid": "2763038", "organism_name": "Clostridium segne", "infraspecific_name": "strain=BX14", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/24", "asm_name": "ASM1428792v1", "asm_submitter": "WFCC-MRCEN World Data Centre for Microoganisms(WDCM)", "gbrs_paired_asm": "GCA_014287925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/287/925/GCF_014287925.1_ASM1428792v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3098902", "genome_size_ungapped": "3098902", "gc_percent": "48.500000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014287925.1-RS_2024_07_15", "annotation_date": "2024-07-15", "total_gene_count": "2844", "protein_coding_gene_count": "2735", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-24", "dateModified": "2020-08-24", "datePublished": "2020-08-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Clostridium segne" ], "sample_taxid": [ "2763038" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Beijing" ], "sample_host_location_id": [], "data_size": "0.877 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3098902", "Number of Sequences": "17", "Longest Sequences (bp)": "358397", "N50 (bp)": "274291", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "48.5", "Number of CDSs": "2802", "Average Protein Length": "318.9", "Coding Ratio (%)": "86.5", "Number of rRNAs": "0", "Number of tRNAs": "58", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Clostridium fessum", "strain": "strain=SNUG30386", "accession": "GCA_003024715.1", "taxid": 2126740, "species_taxid": 2126740, "relation_to_type": "type", "validated": true, "ani": 98.0328, "matched_fragments": 889, "total_fragments": 1024, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseburia hominis", "strain": "strain=A2-183", "accession": "GCA_000225345.1", "taxid": 301301, "species_taxid": 301301, "relation_to_type": "type", "validated": true, "ani": 82.615, "matched_fragments": 131, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia obeum", "strain": "strain=ATCC 29174", "accession": "GCA_025147765.1", "taxid": 40520, "species_taxid": 40520, "relation_to_type": "type", "validated": true, "ani": 80.8277, "matched_fragments": 82, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] lactaris", "strain": "strain=ATCC 29176", "accession": "GCA_000155205.1", "taxid": 46228, "species_taxid": 46228, "relation_to_type": "type", "validated": true, "ani": 79.9644, "matched_fragments": 52, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Ruminococcus] lactaris", "strain": "strain=ATCC 29176", "accession": "GCA_025152405.1", "taxid": 46228, "species_taxid": 46228, "relation_to_type": "type", "validated": true, "ani": 79.8623, "matched_fragments": 52, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia luti", "strain": "strain=DSM 14534", "accession": "GCA_009707925.1", "taxid": 89014, "species_taxid": 89014, "relation_to_type": "suspected-type", "validated": true, "ani": 79.8623, "matched_fragments": 82, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mediterraneibacter butyricigenes", "strain": "strain=KCTC 15684", "accession": "GCA_003574295.1", "taxid": 2316025, "species_taxid": 2316025, "relation_to_type": "type", "validated": true, "ani": 79.7991, "matched_fragments": 86, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia massiliensis", "strain": "strain=GD9", "accession": "GCA_001487165.1", "taxid": 1737424, "species_taxid": 1737424, "relation_to_type": "type", "validated": true, "ani": 79.7968, "matched_fragments": 102, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1-82", "accession": "GCA_900537995.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 79.6823, "matched_fragments": 107, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia wexlerae", "strain": "strain=DSM 19850", "accession": "GCA_025148125.1", "taxid": 418240, "species_taxid": 418240, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6817, "matched_fragments": 86, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blautia wexlerae", "strain": "strain=DSM 19850", "accession": "GCA_000484655.1", "taxid": 418240, "species_taxid": 418240, "relation_to_type": "suspected-type", "validated": true, "ani": 79.66, "matched_fragments": 83, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseburia intestinalis", "strain": "strain=L1-82", "accession": "GCA_000156535.1", "taxid": 166486, "species_taxid": 166486, "relation_to_type": "type", "validated": true, "ani": 79.3785, "matched_fragments": 102, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] aminophilum", "strain": "strain=F", "accession": "GCA_900112885.1", "taxid": 1526, "species_taxid": 1526, "relation_to_type": "type", "validated": true, "ani": 78.0879, "matched_fragments": 107, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Clostridium] aminophilum", "strain": "strain=DSM 10710", "accession": "GCA_000711825.1", "taxid": 1526, "species_taxid": 1526, "relation_to_type": "type", "validated": true, "ani": 78.0375, "matched_fragments": 107, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hungatella hathewayi", "strain": "strain=DSM 13479", "accession": "GCA_025149285.1", "taxid": 154046, "species_taxid": 154046, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1867, "matched_fragments": 121, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterocloster asparagiformis", "strain": "strain=DSM 15981", "accession": "GCA_025149125.1", "taxid": 333367, "species_taxid": 333367, "relation_to_type": "type", "validated": true, "ani": 76.8811, "matched_fragments": 96, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterocloster asparagiformis", "strain": "strain=DSM 15981", "accession": "GCA_000158075.1", "taxid": 333367, "species_taxid": 333367, "relation_to_type": "type", "validated": true, "ani": 76.7316, "matched_fragments": 98, "total_fragments": 1024, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003024715.1", "gtdb_species": "s__Clostridium_Q fessum", "ani": 98.0328, "matched_fragments": 889, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 31, "status": "conclusive" }, { "accession": "GCA_003478355.1", "gtdb_species": "s__UBA3402 sp003478355", "ani": 83.0541, "matched_fragments": 228, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.69", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003478505.1", "gtdb_species": "s__Ventrimonas sp003478505", "ani": 82.8243, "matched_fragments": 217, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.78", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003435375.1", "gtdb_species": "s__Copromonas sp900066535", "ani": 81.8128, "matched_fragments": 239, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.23", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.74", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_003481825.1", "gtdb_species": "s__Ventrimonas sp003481825", "ani": 81.3174, "matched_fragments": 185, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.65", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003480315.1", "gtdb_species": "s__Ventrimonas sp003480315", "ani": 79.9884, "matched_fragments": 192, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_016302185.1", "gtdb_species": "s__Clostridium_Q sp016302185", "ani": 78.3779, "matched_fragments": 186, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_900555625.1", "gtdb_species": "s__Ventrimonas sp900555625", "ani": 78.2727, "matched_fragments": 93, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900547735.1", "gtdb_species": "s__Clostridium_Q sp900547735", "ani": 78.2069, "matched_fragments": 182, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_018377235.1", "gtdb_species": "s__Clostridium_Q sp018377235", "ani": 78.1174, "matched_fragments": 131, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_900626075.1", "gtdb_species": "s__Clostridium_Q transplantifaecale", "ani": 78.0883, "matched_fragments": 180, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000466485.1", "gtdb_species": "s__Clostridium_Q symbiosum", "ani": 77.9717, "matched_fragments": 182, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.81", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCA_900538475.1", "gtdb_species": "s__Ventrimonas sp900538475", "ani": 77.7954, "matched_fragments": 98, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900770345.1", "gtdb_species": "s__Enterocloster sp900770345", "ani": 77.6512, "matched_fragments": 95, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_900770535.1", "gtdb_species": "s__Ventrimonas sp900770535", "ani": 77.5198, "matched_fragments": 96, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.72", "min_intra_species_ani": "98.72", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009911305.1", "gtdb_species": "s__Clostridium_Q sp009911305", "ani": 77.4189, "matched_fragments": 184, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900540335.1", "gtdb_species": "s__Ventrimonas sp900540335", "ani": 77.3382, "matched_fragments": 90, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.37", "min_intra_species_ani": "99.36", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.81", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_001304875.1", "gtdb_species": "s__Ventrisoma faecale", "ani": 77.2753, "matched_fragments": 147, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrisoma", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000235505.1", "gtdb_species": "s__Hungatella_A hathewayi_A", "ani": 77.2422, "matched_fragments": 103, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "96.59", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.86", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_004554205.1", "gtdb_species": "s__Ventrimonas sp004554205", "ani": 76.6319, "matched_fragments": 81, "total_fragments": 1024, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.16, "cell_length": 0.434, "doubling_h": 0.353, "growth_tmp": 33.457, "optimum_tmp": 35.173, "optimum_ph": 6.947, "genome_size": 4165901.003, "gc_content": 29.49, "coding_genes": 3796.985, "rRNA16S_genes": 9.374, "tRNA_genes": 78.312, "gram_stain": 0.945, "sporulation": 0.967, "motility": 0.92, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.944, "thermophilic_range_tmp": 0.055, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Clostridium", "segne" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }